Computing with evolving proteins

Abstract

Dynamic Local Search [1] has been applied to the evolution of interactions between protein-like structures. These are composed of a randomly selected sequence of amino acids that are linked together to form linear polymers in three dimensions. The objective function chosen for optimisation is the potential energy given by a Toy protein model. Proteins fold, move and interact with other chains to minimise their objective function at a given rate, Frate, depending on the sum of the rates fbr re-organisation of their structures. The interaction between different proteins gives a whole range of local attraction/repulsion regimes that result in new structures with new bonds, broken bonds and recursive loops.